Damage to coral and reef habitat caused by dredging at the Port of Miami

Manuscript Figures and Supplementary Figures

Study area and design

Figure 1A. Large scale map

Figure 1B. Small scale map

 

Sedimentation on the reef

Fine sediment deposition rates

 

Figure 2. Deposition of fine sediments in each monitoring area during dredging operations. Horizontal line segments indicate measured rates of fine sediment deposition by each trap over each deployment period. Smooth lines are GAM fits for each monitoring area (±95% CI), colored according to distance from channel. Vertical dotted lines indicate the beginning (2013-11-20) and end (2015-03-16) of dredging operations.

 

Sand cover

 

Figure 3. Percent sand cover at each monitoring area during dredging operations. Points indicate the mean percent sand cover for each transect measured by CPCe analysis, and smooth lines show GAMM fits for each monitoring area (±84% CI). Fitted lines are colored by distance from channel. Vertical dotted lines indicate the beginning (2013-11-20) and end (2015-03-16) of dredging operations.

 

Figure S1. Percent sand cover at each monitoring area during dredging operations. Points indicate the mean percent sand cover for each transect measured by CPCe analysis, and smooth lines show GAMM fits for each monitoring area (±84% CI). Fitted lines are colored by distance from channel. Vertical dotted lines indicate the beginning (2013-11-20) and end (2015-03-16) of dredging operations.

Figure S1 is the same as Figure 3 with the time axis extended to show 2016 data points.

 

Figure S2. Correlation between fine sediment deposition rates and benthic sediment cover during dredging operations at each monitoring area. The left y-axis and solid lines correspond to the fine sediment deposition rate (see Fig. S1), while the right y-axis and dotted lines correspond to percent sand cover (see Fig. 2), with separate panels for each monitoring area. The coefficient of correlation between the two time series is displayed in each panel, along with the lag time (of cover following deposition) for which the highest correlation is observed (up to 120 days). Colors correspond to distance from channel. Blank panels are combinations of reef, direction, and distance for which monitoring data do not exist. Vertical dotted lines indicate the beginning (2013-11-20) and end (2015-03-16) of dredging operations.

Figure S2 presents the same data from Figures 2 and 3, analyzed and visualized together to show their correlation.

 

Total fine sediment deposition

 

Figure 4. Total amount of fine sediments deposited in each monitoring area during dredging operations. Bars indicate the sum of fitted daily fine sediment deposition rates between 2013-11-20 and 2015-03-16 (see Fig. S1) for each monitoring area (± 95% CI). Bars are colored corresponding to distance from channel, and empty spaces indicate areas that were not monitored.

 

Impacts on tagged corals

Coral burial

 

Figure 5. Probability of partial or complete coral burial by sediments in each monitoring area during dredging operations. Points indicate the proportion of living tagged corals in each monitoring area observed on a given date with the condition codes PBUR (partial burial) or BUR (complete burial). Lines represent GAMM fits for each monitoring area (±84% CI) colored by distance from channel. Vertical dotted lines indicate the beginning (2013-11-20) and end (2015-03-16) of dredging operations.

 

Figure S3. Probability of partial or complete coral burial by sediments in each monitoring area during dredging operations. Points indicate the proportion of living tagged corals in each monitoring area observed on a given date with the condition codes PBUR (partial burial) or BUR (complete burial). Lines represent GAMM fits for each monitoring area (±84% CI) colored by distance from channel. Vertical dotted lines indicate the beginning (2013-11-20) and end (2015-03-16) of dredging operations.

Figure S3 is the same as Figure 5, but with the time axis extended to show the 2016 data points.

 

Partial mortality

 

Figure S4. Coral partial mortality due to sedimentation in each monitoring area throughout dredging operations. Bars indicate the predicted probability (±95% CI) of tagged corals being observed with the condition code PM (partial mortality due to sedimentation) at any point through March 2015 (the final month of dredging operations). Bar colors correspond to distance from channel, and empty spaces indicate areas that were not monitored.

 

Figure 6. Relationship between total fine sediment deposition and coral partial mortality during dredging operations. Points indicate, for each monitoring area, the total amount of fine sediments deposited during dredging (±95% CI; see Fig. 3) on the x-axis, and the probability of partial mortality (±95% CI; see Fig. S3) on the y-axis. Points are labeled corresponding to reef region (SIR = sourthern inner reef, NIR = northern inner reef, SMR = southern middle reef, NMR = northern middle reef, SOR = southern outer reef, NOR = northern outer reef) and colored corresponding to distance from channel. The fitted dose-response curve follows a four parameter type two Weibull function weighted inversely by the SE of partial mortality estimates.

 

Total mortality

 

Figure S5. Total mortality of non-disease-susceptible coral species in each monitoring area throughout dredging operations. Bars indicate the predicted probability (±95% CI) of tagged corals being observed with the condition code PM (partial mortality due to sedimentation) at any point through March 2015 (the final month of dredging operations). Bar colors correspond to distance from channel, and empty spaces indicate areas that were not monitored.

 

Impacts on reef habitat

Coral density

 

Figure 7. Density of corals ≥3cm within 500m from the channel in each monitoring region before and after dredging operations. Data ‘before’ dredging were collected in 2009 and 2013, and data after dredging were collected in 2015-2017. GLMM fits are shown as lines for the regions and times in which data were collected at >2 points beyond 50m, and otherwise as points including only data from within 50m of the channel. Shaded regions and error bars represent 84% CI’s. Text annotations indicate the results of tests for differences between timepoints at 20m and 300m from the channel (*** = p < 0.0001; ns = not significantly different).

 

Figures S6. Density of small corals (1-2cm) within 500m from the channel in each monitoring region before and after dredging operations. Data ‘before’ dredging were collected in 2009, and data after dredging were collected in 2016-2017. GLMM fits are shown as lines for the regions and times in which data were collected at >2 points beyond 50m. Shaded regions and error bars represent 84% CI’s. Text annotations indicate the results of tests for differences between timepoints at 20m and 300m from the channel (. = p < 0.1; * = p < 0.05; ns = not significantly different).

 

Coral size-frequency

 

Figure 8. Size frequency distribution of corals before and after dredging. For the northern and southern middle and outer reefs, histograms show the relative proportion of corals within 100m of the channel with a given maximum diameter. P-values on each panel are based on a Kruskal-Wallis test for a difference in mean diameter between the two timepoints.

 

Figure 8 - alternative. Alternative version of Figure 8, with absolute density instead of relative proportion on y-axis.

 

Sediment depth

 

Figure 9. Depth of sediments in relation to channel measured ~2 years after dredging operations. Dots represent individual sediment depth measurements along transects, jittered around the distance from the center of the transect to the channel in each monitoring region (no data available for the inner reef). Lines represent quantile regressions across transects as a function of log(distance from channel), e.g., the percent of reef area with sediments measuring at least a given depth.

 

Sand cover before and after dredging at individual sites

 

Figure S7. Percent cover before (2013) and after dredging (2016) at the three permanent monitoring sites for which both before and after data were collected. Bars indicate the mean percent sand based on CPCe analysis, and error bars represent standard deviation.